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- Eriksson, Susanne
(författare)
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Genetic analysis of 'breeding field test status' in Icelandic horses
- 2011
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Ingår i: Journal of Animal Breeding and Genetics. - : Wiley. - 0931-2668 .- 1439-0388. ; 128, s. 124-132
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Tidskriftsartikel (refereegranskat)abstract
- P>Genetic evaluation of Icelandic horses is currently based on results from breeding field tests where riding ability and conformation of the horses are evaluated over the course of 1-2 days. Only a small part of registered horses attend these field tests, and it can be assumed that these are not a random sample of the population. In this study, the trait test status was introduced, describing whether a horse was assessed in a breeding field test. This trait was analysed to find out whether it has a genetic variation and how it correlates genetically to other traits in the breeding goal. Breeding field test data included 39 443 mares born in Iceland in 1990-2001, of which 7431 were assessed in the period 1994-2007. The trait was defined in relation to age, gender and stud of horses. Variance and covariance components were estimated using the Markov Chain Monte Carlo method by applying the Gibbs sampler procedure in the DMU program. Three multivariate analyses were performed where the test status trait was analysed with breeding field test traits. Animal models and sire models were applied. Based on estimated heritabilities (0.51-0.67) and genetic correlations (0.00-0.87), the test status trait showed significant genetic variation and was strongly correlated to some traits. The test status trait reflects preselection in the breeding field test traits and should be included in the genetic evaluation to enhance the procedure, reduce selection bias and increase accuracy of the estimation.
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- Halkjer Jakobsen, Jette
(författare)
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Udder health and female fertility traits are favourably correlated and support each other in multi-trait evaluations
- 2011
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Ingår i: Journal of Animal Breeding and Genetics. - : Wiley. - 0931-2668 .- 1439-0388. ; 128, s. 174-182
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Tidskriftsartikel (refereegranskat)abstract
- P>Genetic parameters were estimated for protein yield (PY), clinical mastitis (CM), somatic cell score, number of inseminations (NI) and days from calving to first insemination (CFI) in first-parity Swedish Red cows by series of tri-variate linear animal models. The heritability of PY was moderate (0.34 +/- 0.004), and the heritabilities of the functional traits were all low (0.014 +/- 0.001-0.14 +/- 0.004). The genetic correlation between CM and CFI (0.38 +/- 0.05) was stronger than the correlation between CM and NI (0.05 +/- 0.06), perhaps because CM and CFI usually are observed in early lactation when the cow is likely to be in negative energy balance, whereas NI generally is recorded when the cow is not in negative energy balance any more. The genetic correlation between NI and CFI was very close to zero (-0.002 +/- 0.05), indicating that these two fertility traits have different genetic backgrounds. All genetic correlations between PY and the functional traits were moderate and unfavourable, ranging from 0.22 +/- 0.02 to 0.47 +/- 0.03. In addition, the effect of including genetic and phenotypic correlations between the trait groups milk production, udder health and female fertility on the accuracy of the selection index was quantified for a heifer, a cow and a proven bull. The difference between the accuracy obtained by multi-trait and single-trait evaluations was largest for the cow (0.012) and small for the heifer and the bull (0.006 and 0.004) because the phenotype of the cow for one trait could assist in predicting the Mendelian sampling term for a correlated trait.
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- Malm, Sofia, et al.
(författare)
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Efficient selection against categorically scored hip dysplasia in dogs is possible using best linear unbiased prediction and optimum contribution selection: a simulation study
- 2013
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Ingår i: Journal of Animal Breeding and Genetics. - : Wiley. - 0931-2668 .- 1439-0388. ; 130, s. 154-164
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Tidskriftsartikel (refereegranskat)abstract
- Breeding to reduce the prevalence of categorically scored hip dysplasia (HD), based on phenotypic assessment of radiographic hip status, has had limited success. The aim of this study was to evaluate two selection strategies for improved hip status: truncation selection based on phenotypic record versus best linear unbiased prediction (BLUP), using stochastic simulation and selection scenarios resembling those in real dog populations. In addition, optimum contribution selection (OCS) was evaluated. Two traits were considered: HD (as a categorical trait with five classes and a heritability of 0.45 on the liability scale) and a continuous trait (with a heritability of 0.25) intended to represent other characteristics in the breeding goal. A population structure mimicking that in real dog populations was modelled. The categorical nature of HD caused a considerably lower genetic gain compared to simulating HD as a continuous trait. Genetic gain was larger for BLUP selection than for phenotypic selection in all scenarios. However, BLUP selection resulted in higher rates of inbreeding. By applying OCS, the rate of inbreeding was lowered to about the same level as phenotypic selection but with increased genetic improvement. For efficient selection against HD, use of BLUP breeding values should be prioritized. In small populations, BLUP should be used together with OCS or similar strategy to maintain genetic variation.
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- Rius-Vilarrasa, Elisenda Rius, et al.
(författare)
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Influence of model specifications on the reliabilities of genomic prediction in a Swedish-Finnish red breed cattle population
- 2012
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Ingår i: Journal of Animal Breeding and Genetics. - : Wiley. - 0931-2668 .- 1439-0388. ; 129, s. 369-379
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Tidskriftsartikel (refereegranskat)abstract
- Using a combined multi-breed reference population, this study explored the influence of model specification and the effect of including a polygenic effect on the reliability of genomic breeding values (DGV and GEBV). The combined reference population consisted of 2986 Swedish Red Breed (SRB) and Finnish Ayrshire (FAY) dairy cattle. Bayesian methodology (common prior and mixture models with different prior distribution settings for the marker effects) as well as a best linear unbiased prediction with a genomic relationship matrix [genomic best linear unbiased predictor (GBLUP)] was used in the prediction of DGV. Mixture models including a polygenic effect were used to predict GEBV. In total, five traits with low, high and medium heritability were analysed. For the models using a mixture prior distribution, reliabilities of DGV tended to decrease with an increasing proportion of markers with small effects. The influence of the inclusion of a polygenic effect on the reliability of DGV varied across traits and model specifications. Average correlation between DGV with the Mendelian sampling term, across traits, was highest (R2 = 0.25) for the GBLUP model and decreased with increasing proportion of markers with large effects. Reliabilities increased when DGV and parent average information were combined in an index. The GBLUP model with the largest gain across traits in the reliability of the index achieved the highest DGV mean reliability. However, the polygenic models showed to be less biased and more consistent in the estimation of DGV regardless of the model specifications compared with the mixture models without the polygenic effect.
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| 8. |
- Rönnegård, Lars, et al.
(författare)
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Non-iterative variance component estimation in QTL analysis
- 2009
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Ingår i: Journal of Animal Breeding and Genetics. - : Wiley. - 0931-2668 .- 1439-0388. ; 126:2, s. 110-116
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Tidskriftsartikel (refereegranskat)abstract
- In variance component quantitative trait loci (QTL) analysis, a mixed model is used to detect the most likely chromosome position of a QTL. The putative QTL is included as a random effect and a method is needed to estimate the QTL variance. The standard estimation method used is an iterative method based on the restricted maximum likelihood (REML). In this paper, we present a novel non-iterative variance component estimation method. This method is based on Henderson's method 3, but relaxes the condition of unbiasedness. Two similar estimators were compared, which were developed from two different partitions of the sum of squares in Henderson's method 3. The approach was compared with REML on data from a European wild boar x domestic pig intercross. A meat quality trait was studied on chromosome 6 where a functional gene was known to be located. Both partitions resulted in estimated QTL variances close to the REML estimates. From the non-iterative estimates, we could also compute good approximations of the likelihood ratio curve on the studied chromosome.
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| 10. |
- Arvelius, Per
(författare)
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How Swedish breeders can substantially increase the genetic gain for the English Setter’s hunting traits
- 2013
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Ingår i: Journal of Animal Breeding and Genetics. - : Wiley. - 0931-2668 .- 1439-0388. ; 130, s. 142-153
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Tidskriftsartikel (refereegranskat)abstract
- In both Sweden (Swe) and Norway (Nor), the English Setter is used for hunting. Similar field trials are arranged to give breeders information on the dogs' hunting abilities. Our main objective was to study if a joint Swe- Nor genetic evaluation can improve accuracy compared with estimation of breeding values on a national level only. Genetic parameters for six hunting traits were estimated in univariate (within country) and bivariate (across country, of equivalent traits between countries and joint pedigree) analyses utilizing 3620 Swe records from 685 dogs and 94 414 Nor records from 7175 dogs. A mixed linear animal model was used, including fixed effects of sex, type of trial, year, month and interaction between age and class of trial, and random effects of animal, permanent environment, judge and residual. Heritabilities ranged from 0.07 to 0.13 for Swe and from 0.08 to 0.18 for Nor. The accuracies were higher in the bivariate analyses, especially for dogs with Swe trial results with an average increase of 19%. If comparing selection based on a joint genetic evaluation over phenotypic results alone (which is today's method), the potential genetic gain in Swe was almost doubled. Our results suggest that a joint genetic evaluation is especially advantageous for a population with limited information, such as the English Setter population in Swe. However, it should also be beneficial for Norwegian breeders because it makes it easier for them to select Swedish dogs, potentially resulting in faster genetic gain and lowered inbreeding rate.
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